Niche Partitioning of the N Cycling Microbial Community of an Offshore Oxygen Deficient Zone.
Niche Partitioning of the N Cycling Microbial Community of an Offshore Oxygen Deficient Zone.
复制标题
DOI：
10.3389/fmicb.2017.02384
复制
发表时间：
2017
影响因子：
5.2
通讯作者：
Rocap G
中科院分区：
文献类型：
--
作者：
Fuchsman CA;Devol AH;Saunders JK;McKay C;Rocap G
海洋缺氧区（ODZs）的微生物群落通过将营养物质转化为N2O和N2，承担了高达一半的海洋氮损失。这种氮的损失是由多种微生物组成的联合体完成的，其中许多微生物仍未被培养。在这里，我们对来自东热带北太平洋（ETNP） ODZ的水柱和bbb30 μm颗粒的宏基因组中缺氧N循环所有步骤的基因进行了表征。我们使用一种方法，允许系统发育鉴定和基因丰度的半定量评估从单个生物体，并把这些结果在化学测量和速率数据的背景下，从同一位置。反硝化基因在bbb30 μm颗粒中富集，即使在氧化素中也是如此，而厌氧氨氧化菌在颗粒上并不丰富。反硝化的许多步骤是由不同分布的多个种型编码的。值得注意的是，三种N2O还原酶（nosZ），每一种都没有培养的亲戚，居住在不同的生态位；一个是自由生活的，一个在颗粒上占主导地位，一个具有自养s氧化细菌中发现的C端延伸。在某些深度，30%的群落具有亚硝酸盐还原酶。与SAR11相关的nirK OTU解释了这种丰度的大部分原因。在ODZ中发现的唯一能将NO还原为N2O的细菌基因是一种与先前假设的“一氧化氮歧化酶”相关的qnorB基因，该基因在氧化甲烷的同时直接产生N2。然而，在已发表的许多不氧化甲烷的细菌基因组中也发现了类似的qnorb样基因，并且这里的qnorb样基因与甲烷氧化基因的存在无关。与N2O浓度的相关性表明，这些qnorb样基因可能促进ODZ中NO还原为N2O。在氧跃层中，水柱中未检测到qnorb样基因，并且氨氧化产生N2O的估计速率不足以支持观察到的氧跃层N2O最大值。然而，qnorb样基因和nosZ基因同时存在于氧斜区的颗粒中，表明颗粒来源为N2O和N2。总之，我们的分析提供了低氧氮循环中不同参与者的整体观点。
Microbial communities in marine oxygen deficient zones (ODZs) are responsible for up to half of marine N loss through conversion of nutrients to N2O and N2. This N loss is accomplished by a consortium of diverse microbes, many of which remain uncultured. Here, we characterize genes for all steps in the anoxic N cycle in metagenomes from the water column and >30 μm particles from the Eastern Tropical North Pacific (ETNP) ODZ. We use an approach that allows for both phylogenetic identification and semi-quantitative assessment of gene abundances from individual organisms, and place these results in context of chemical measurements and rate data from the same location. Denitrification genes were enriched in >30 μm particles, even in the oxycline, while anammox bacteria were not abundant on particles. Many steps in denitrification were encoded by multiple phylotypes with different distributions. Notably three N2O reductases (nosZ), each with no cultured relative, inhabited distinct niches; one was free-living, one dominant on particles and one had a C terminal extension found in autotrophic S-oxidizing bacteria. At some depths >30% of the community possessed nitrite reductase nirK. A nirK OTU linked to SAR11 explained much of this abundance. The only bacterial gene found for NO reduction to N2O in the ODZ was a form of qnorB related to the previously postulated “nitric oxide dismutase,” hypothesized to produce N2 directly while oxidizing methane. However, similar qnorB-like genes are also found in the published genomes of many bacteria that do not oxidize methane, and here the qnorB-like genes did not correlate with the presence of methane oxidation genes. Correlations with N2O concentrations indicate that these qnorB-like genes likely facilitate NO reduction to N2O in the ODZ. In the oxycline, qnorB-like genes were not detected in the water column, and estimated N2O production rates from ammonia oxidation were insufficient to support the observed oxycline N2O maximum. However, both qnorB-like and nosZ genes were present within particles in the oxycline, suggesting a particulate source of N2O and N2. Together, our analyses provide a holistic view of the diverse players in the low oxygen nitrogen cycle.